RNA degradome analysis reveals substrates of NYN-domain containing DNE1 endoribonuclease in Arabidopsis

To gain insight into the functional role of DNE1 in cytoplasmic mRNA decay, we performed Parallel Analysis of RNA Ends (PARE) and Global Mapping of Uncapped and Cleaved Transcripts (GMUCT) analysis to identify DNE1-dependent cleavage sites based on their sensitivity to XRN4 within the Arabidopsis transcriptome Overall design: RNA degradome analysis (ATH1036-41; ATH1082-87): Comparing the RNA decay profiles allowed for the detection of abundant monophosphorylated 5' ends (5'P) within transcripts in xrn4 that were absent in dne1xrn4. Thereby, we identified a number of 5'P sites that were dependent on DNE1 activity. RNA-seq analysis (ATH1046-57): For comparing full-length transcript abundances between xrn4 and dne1xrn4.